“Ecogenomic sensors” were originally conceived of as field deployable devices that would use molecular probe techniques to detect specific organisms, genes and gene products in situ. Early versions of this concept imagined arrays of these devices that were embedded in a larger environmental observing system, providing a rich context in which to view the sensor output. By making results of analyses available in real-time, and allowing users to redirect activity of those devices “on the fly”, it was imagined that investigators could extend their work beyond what could be accomplished using ship and shore based laboratories alone, thus opening a new window for observing biological processes in the sea (Scholin, 2013).
The Environmental Sample Processor (ESP) is a robotic device that exemplifies the ecogenomic sensor concept; it combines autonomous sample collection capability with real-time molecular analytical detection functionality (Preston et al. 2011, Ussler et al. 2013, Robidart et al. 2014). The ESP can also be used to preserve samples for more in-depth, laboratory-based analyses upon instrument retrieval (Ottesen et al. 2014).
Although the ESP has been used successfully in a variety of settings, it is not readily accessible to researchers because of its cost, and the training needed to deploy and operate it. This project was designed to address these challenges by acquiring an instrument that will be dedicated to GBMF-approved investigators given operational support provided by the ESP team at the Monterey Bay Aquarium Institute. In addition, the ESP’s fluidic intake will be modified to enable sampling to 200m below the sea surface (the current configuration only allows the ESP to operate to depths of 50m; an external sampling module is required for deeper operations). Increasing the depth rating of the core ESP is expected to create new opportunities for deploying the instrument in a wide range of settings.
Ottesen, E.A., Young, C.R., Gifford, S.M., Eppley, J.M., Marin III, R., Schuster, S.C., Scholin, C.A., DeLong, E.F. 2014. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science 345: 207-212. (DOI: 10.1126/science.1252476).
Preston, C.M., A. Harris, J. P. Ryan, B. Roman, R. Marin III, S. Jensen, C. Everlove, J. Birch, J. M. Dzenitis, D. Pargett, M. Adachi, K. Turk, J. P. Zehr, C. A. Scholin. 2011. Underwater application of quantitative PCR on an ocean mooring. PLoS ONE 6(8): e22522. doi:10.1371/journal.pone.0022522
Robidart, J.C., Church, M.J., Ryan, J.P., Ascani, F., Wilson, S.T., Bombar, D., Marin, R III, Richards, K.J., Karl, D.M., Scholin, C.A., Zehr, J.P. 2014. Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal 8, 1175–1185 (doi:10.1038/ismej.2013.244)
Scholin C.A. 2013. Ecogenomic Sensors. In: Levin S.A. (ed.) Encyclopedia of Biodiversity, second edition, Volume 2, pp. 690-700. Waltham, MA: Academic Press.
Ussler, W. III, P. Tavormina, C. Preston, R. Marin III, D. Pargett, S. Jensen, B. Roman, S. Shah, P.R. Girguis, J.M. Birch, V. Orphan, C. Scholin, 2013. Autonomous in situ quantitative PCR amplification of aerobic methanotroph genes in the deep sea. Environ. Sci. Technology 47:9339−9346 (dx.doi.org/10.1021/es4023199 )